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Old 06-20-2010, 08:43 AM   #1
Junior Member
Location: baltimore

Join Date: Feb 2009
Posts: 9
Default sff_extract question

Hi all,

I'm trying to run sff_extract on a set of files that are stored in one location and want the output to be re-directed to another location (for storage reasons). The default settings seem to be writing the outputs to the same location as the input. Also, is there a way I can output *only* fasta files after clipping with -c option?

Thanks much!
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Old 06-20-2010, 10:31 PM   #2
Jose Blanca
Location: Valencia, Spain

Join Date: Aug 2009
Posts: 70

You can tell sff_extract where to store and how to name every output file:

-s FILE, --seq_file=FILE
output sequence file name
-q FILE, --qual_file=FILE
output quality file name
-x FILE, --xml_file=FILE
output ancillary xml file name

For instance you could do:

-s /some/dir/seqs.fasta -q /some/dir/seqs.qual -x /dev/null

Best regards.
Jose Blanca is offline   Reply With Quote

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